ClinVar Genomic variation as it relates to human health
NM_000454.5(SOD1):c.140A>G (p.His47Arg)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000454.5(SOD1):c.140A>G (p.His47Arg)
Variation ID: 14764 Accession: VCV000014764.11
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 21q22.11 21: 31663857 (GRCh38) [ NCBI UCSC ] 21: 33036170 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Apr 4, 2013 Oct 8, 2024 Jan 22, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000454.5:c.140A>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000445.1:p.His47Arg missense NC_000021.9:g.31663857A>G NC_000021.8:g.33036170A>G NG_008689.1:g.9236A>G LRG_652:g.9236A>G LRG_652t1:c.140A>G LRG_652p1:p.His47Arg P00441:p.His47Arg - Protein change
- H47R
- Other names
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H46R
- Canonical SPDI
- NC_000021.9:31663856:A:G
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
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The frequency of the allele represented by this VCV record.
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- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
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The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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SOD1 | - | - |
GRCh38 GRCh37 |
206 | 321 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
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The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Pathogenic (3) |
criteria provided, multiple submitters, no conflicts
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Jan 22, 2024 | RCV000015886.29 | |
Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Jan 18, 2021 | RCV000281824.3 | |
Pathogenic (1) |
criteria provided, single submitter
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Jan 1, 2022 | RCV001843454.1 | |
SOD1-related disorder
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Pathogenic (1) |
no assertion criteria provided
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Mar 12, 2024 | RCV004745158.1 |
Submissions - Germline
Classification
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The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
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The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
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The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
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This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Pathogenic
(Jan 01, 2022)
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criteria provided, single submitter
Method: research
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Amyotrophic Lateral Sclerosis
Affected status: yes
Allele origin:
germline
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Dept. of Medical Genetics, Telemark Hospital Trust, Telemark Hospital Trust
Accession: SCV002103152.1
First in ClinVar: Mar 12, 2022 Last updated: Mar 12, 2022 |
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Pathogenic
(Jan 22, 2024)
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criteria provided, single submitter
Method: clinical testing
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Amyotrophic lateral sclerosis type 1
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000823424.6
First in ClinVar: Oct 10, 2018 Last updated: Feb 14, 2024 |
Comment:
This sequence change replaces histidine, which is basic and polar, with arginine, which is basic and polar, at codon 47 of the SOD1 protein (p.His47Arg). … (more)
This sequence change replaces histidine, which is basic and polar, with arginine, which is basic and polar, at codon 47 of the SOD1 protein (p.His47Arg). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with autosomal dominant amyotrophic lateral sclerosis (ALS) (PMID: 7836951, 8298637, 14506936, 22475618, 25025039). It has also been observed to segregate with disease in related individuals. This variant is also known as p.His46Arg. ClinVar contains an entry for this variant (Variation ID: 14764). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt SOD1 protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects SOD1 function (PMID: 7836951, 8298637, 10889018, 18951903, 19483195, 19635794). For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Jun 27, 2016)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV000329738.5
First in ClinVar: Dec 06, 2016 Last updated: Dec 06, 2016 |
Comment:
The H47R variant in the SOD1 gene, also reported as H46R due to alternate nomenclature, was initially found to co-segregate with a slowly progressive autosomal … (more)
The H47R variant in the SOD1 gene, also reported as H46R due to alternate nomenclature, was initially found to co-segregate with a slowly progressive autosomal dominant form of amyotrophic lateral sclerosis in multiple affected individuals from two unrelated Japanese families (Aoki et al., 1993). The H47R variant has also been reported to co-segregate with a dominant form of hereditary motor neuropathy (Ostern et al., 2012; Hoyer et al., 2014). The H47R variant was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The H47R variant is a conservative amino acid substitution, which occurs at a position that is conserved across species. Functional studies demonstrate that results in a conformational change of the SOD1 protein resulting in aberrant binding activity (Fujisawa et al., 2012). We interpret H47R as a pathogenic variant. (less)
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Pathogenic
(Jan 18, 2021)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
unknown
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Athena Diagnostics
Accession: SCV001880022.1
First in ClinVar: Sep 19, 2021 Last updated: Sep 19, 2021 |
Comment:
This variant was not reported in large, multi-ethnic, general populations (http://gnomad.broadinstitute.org). This variant has been identified in multiple unrelated individuals with clinical features associated with … (more)
This variant was not reported in large, multi-ethnic, general populations (http://gnomad.broadinstitute.org). This variant has been identified in multiple unrelated individuals with clinical features associated with this gene. This variant is also referred to as p.His46Arg in published literature. Assessment of experimental evidence suggests this variant results in abnormal protein function. This variant was shown to impair the metal binding activity of the protein (PMID: 10889018, 19635794, 18951903). Computational tools predict that this variant is damaging. (less)
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Pathogenic
(Apr 20, 2023)
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criteria provided, single submitter
Method: clinical testing
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Amyotrophic lateral sclerosis type 1
(Sporadic)
Affected status: yes
Allele origin:
de novo
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Suna and Inan Kirac Foundation Neurodegeneration Research Laboratory, Koc University
Accession: SCV003918821.1
First in ClinVar: Apr 30, 2023 Last updated: Apr 30, 2023 |
Comment:
The His47Arg variant of SOD1 gene is the most frequent SOD1 mutation in Asian ALS patients (Arisato 2003, Tang 2019). The mutation first described in … (more)
The His47Arg variant of SOD1 gene is the most frequent SOD1 mutation in Asian ALS patients (Arisato 2003, Tang 2019). The mutation first described in two Japanese ALS families and is found to be disruptive for protein function (Aoki 1994). (less)
Clinical Features:
Lower limb muscle weakness (present) , Abnormal lower motor neuron morphology (present) , Bulbar signs (absent) , Upper motor neuron dysfunction (absent)
Age: 30-39 years
Sex: female
Ethnicity/Population group: Caucasian
Geographic origin: Turkey
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Pathogenic
(Jul 18, 2000)
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no assertion criteria provided
Method: literature only
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AMYOTROPHIC LATERAL SCLEROSIS 1
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000036153.1
First in ClinVar: Apr 04, 2013 Last updated: Apr 04, 2013 |
Comment on evidence:
In 2 Japanese families with unusually slow progression of ALS (105400), Aoki et al. (1993) found an A-to-G transition in exon 2 of the SOD1 … (more)
In 2 Japanese families with unusually slow progression of ALS (105400), Aoki et al. (1993) found an A-to-G transition in exon 2 of the SOD1 gene that resulted in a his46-to-arg (H46R) substitution. His46 is a highly conserved residue within the active site of the enzyme, and the mutation was predicted to affect copper binding. The mutation was not found in 27 Japanese patients with sporadic ALS or 57 unrelated normal control subjects. Functional expression studies showed that the mutant enzyme activity was reduced by about 20%. Aoki et al. (1993) suggested that the H46R substitution influences only the active site and does not interfere with dimer formation, which had been reported for other SOD1 mutations. Affected individuals showed a relatively mild form of the disorder, with symptoms appearing in the arms more than 5 years after onset and bulbar signs appearing more than 8 years after initial symptoms in the legs. The mean survival after onset was 17.3 years in the Japanese cases as compared with 1.5 years and 2.4 years in Caucasian families and 2.5 years in Japanese families with different mutations. Aoki et al. (1994) presented in greater detail the data reported by Aoki et al. (1993). Liu et al. (2000) determined that mutant H46R SOD1 binds neither Cu(2+) nor Co(2+) at the native copper-binding site, but forms a new copper-binding site at cys111 on the surface near the site of dimer formation. Insertion of copper ions into SOD1 under normal conditions in vivo requires the presence of a copper chaperone, CCS (603864). Liu et al. (2000) hypothesized that cys111 is an intermediate docking site for Cu(2+) during SOD1 biosynthesis and that it transfers Cu(2+) to the final destination in the active site of the wildtype enzyme. (less)
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Pathogenic
(Mar 12, 2024)
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no assertion criteria provided
Method: clinical testing
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SOD1-related condition
Affected status: unknown
Allele origin:
germline
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PreventionGenetics, part of Exact Sciences
Accession: SCV005366940.1
First in ClinVar: Oct 08, 2024 Last updated: Oct 08, 2024 |
Comment:
The SOD1 c.140A>G variant is predicted to result in the amino acid substitution p.His47Arg. This variant, previously referred to as p.His46Arg using legacy nomenclature, has … (more)
The SOD1 c.140A>G variant is predicted to result in the amino acid substitution p.His47Arg. This variant, previously referred to as p.His46Arg using legacy nomenclature, has been reported to be causative for ALS in the heterozygous state (Aoki et al. 1993, PubMed ID: 8298637; Niemann et al 2004. PubMed ID: 15258228). The c.140A>G variant has been interpreted as pathogenic in the ClinVar database (https://www.ncbi.nlm.nih.gov/clinvar/variation/14764/). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. This variant is interpreted as pathogenic. (less)
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Genetic Spectrum and Variability in Chinese Patients with Amyotrophic Lateral Sclerosis. | Liu ZJ | Aging and disease | 2019 | PMID: 31788332 |
Better survival in female SOD1-mutant patients with ALS: a study of SOD1-related natural history. | Tang L | Translational neurodegeneration | 2019 | PMID: 30637102 |
H46R SOD1 mutation is consistently associated with a relatively benign form of amyotrophic lateral sclerosis with slow progression. | Zou ZY | Amyotrophic lateral sclerosis & frontotemporal degeneration | 2016 | PMID: 27348463 |
Next-generation sequencing of 28 ALS-related genes in a Japanese ALS cohort. | Nakamura R | Neurobiology of aging | 2016 | PMID: 26742954 |
Genetic diagnosis of Charcot-Marie-Tooth disease in a population by next-generation sequencing. | Høyer H | BioMed research international | 2014 | PMID: 25025039 |
Hereditary motor neuron disease in a large Norwegian family with a "H46R" substitution in the superoxide dismutase 1 gene. | Østern R | Neuromuscular disorders : NMD | 2012 | PMID: 22475618 |
The epidemiology of CuZn-SOD mutations in Germany: a study of 217 families. | Rabe M | Journal of neurology | 2010 | PMID: 20309572 |
A common property of amyotrophic lateral sclerosis-associated variants: destabilization of the copper/zinc superoxide dismutase electrostatic loop. | Molnar KS | The Journal of biological chemistry | 2009 | PMID: 19635794 |
Variation in aggregation propensities among ALS-associated variants of SOD1: correlation to human disease. | Prudencio M | Human molecular genetics | 2009 | PMID: 19483195 |
Flexor-dominant myopathic phenotype in patients with His46Arg substitution in the Cu/Zn superoxide dismutase gene. | Yamashita S | Journal of the neurological sciences | 2009 | PMID: 19344917 |
Unfolding and folding kinetics of amyotrophic lateral sclerosis-associated mutant Cu,Zn superoxide dismutases. | Rumfeldt JA | Journal of molecular biology | 2009 | PMID: 18951903 |
Slowly progressing amyotrophic lateral sclerosis caused by H46R SOD1 mutation. | Holmøy T | European neurology | 2007 | PMID: 17483589 |
Familial ALS-superoxide dismutases associate with mitochondria and shift their redox potentials. | Ferri A | Proceedings of the National Academy of Sciences of the United States of America | 2006 | PMID: 16945901 |
Familial amyotrophic lateral sclerosis with His46Arg mutation in Cu/Zn superoxide dismutase presenting characteristic clinical features and Lewy body-like hyaline inclusions. | Ohi T | Journal of the neurological sciences | 2004 | PMID: 15465081 |
Familial ALS in Germany: origin of the R115G SOD1 mutation by a founder effect. | Niemann S | Journal of neurology, neurosurgery, and psychiatry | 2004 | PMID: 15258228 |
Clinical and pathological studies of familial amyotrophic lateral sclerosis (FALS) with SOD1 H46R mutation in large Japanese families. | Arisato T | Acta neuropathologica | 2003 | PMID: 14517684 |
Sixteen novel mutations in the Cu/Zn superoxide dismutase gene in amyotrophic lateral sclerosis: a decade of discoveries, defects and disputes. | Andersen PM | Amyotrophic lateral sclerosis and other motor neuron disorders : official publication of the World Federation of Neurology, Research Group on Motor Neuron Diseases | 2003 | PMID: 14506936 |
Clinical features and neuropathological findings of familial amyotrophic lateral sclerosis with a His46Arg mutation in Cu/Zn superoxide dismutase. | Ohi T | Journal of the neurological sciences | 2002 | PMID: 11997070 |
Copper(2+) binding to the surface residue cysteine 111 of His46Arg human copper-zinc superoxide dismutase, a familial amyotrophic lateral sclerosis mutant. | Liu H | Biochemistry | 2000 | PMID: 10889018 |
Familial amyotrophic lateral sclerosis (ALS) in Japan associated with H46R mutation in Cu/Zn superoxide dismutase gene: a possible new subtype of familial ALS. | Aoki M | Journal of the neurological sciences | 1994 | PMID: 7836951 |
Mild ALS in Japan associated with novel SOD mutation. | Aoki M | Nature genetics | 1993 | PMID: 8298637 |
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Text-mined citations for rs121912443 ...
HelpRecord last updated Oct 13, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.